Open tabs

Welcome, briefly captive audience before the next click that takes you far, far away to a server in Bangalore or Vladivostok.

I am going to do a tab-and-link dump here (a.k.a. structured procrastination). What I think is important enough to be reading right now, so that I keep a dozen or so tabs open for these papers. In addition, there were, until just now when I started cleaning up, tabs devoted to one blog post I hadn’t felt like I had finished reading or thinking about, an order of a new dishwasher, and directions to the venue at which I was going to be part of a wind ensemble concert Friday night, though it was cancelled in extremis yesterday. And numerous temporary tabs that get opened and closed – ever take a look at your history (Ctrl-Alt-H in Firefox)? Sobering. 248 clicks to different links yesterday morning, 176 in a similar time frame today.*

Without further ado:

News of the WeekScience 28 January 2011: Vol. 331 no. 6016 pp. 382-383 DOI: 10.1126/science.331.6016.382-a – what interested me here, was the announcement that Roche made, that a pharmacological inhibitor, RG7204 by the biotech company Plexxikon, extends life of patients with aggressive melanoma. Presumably only the ones with activating mutations in BRAF, which is an intracellular signaling effector in a number of growth factor pathways. I study among other things, the large congenital melanocytic nevus, a precursor condition in some cases to pediatric melanoma, which can be nasty stuff indeed and doesn’t respond well to current chemotherapies. If certain cases can rapidly be diagnosed as having constitutively active BRAF then they would also be good candidates for responding to this drug. I don’t know if this phase III trial includes children, but I highly doubt it.

In the closely watched phase III trial, patients with the B-RAF mutation who received the drug lived significantly longer and their tumors grew more slowly compared with patients who received a standard chemotherapy drug, Roche officials announced in a press release. But the company did not disclose how much longer patients lived on average. Full results will be reported later this year at a meeting. Patients receiving the standard drug will now be offered the option of switching to RG7204.

Cardiac neural crest orchestrates remodeling and functional maturation of mouse semilunar valves by Rajan Jain, Kurt A. Engleka, Stacey L. Rentschler, Lauren J. Manderfield, Li Li, Lijun Yuan, Jonathan A. Epstein.  J Clin Invest. 2011;121(1):422–430 doi:10.1172/JCI44244 (Open Access, yay!)

The FGF-BMP Signaling Axis Regulates Outflow Tract Valve Primordium Formation by Promoting Cushion Neural Crest Cell Differentiation by Jue Zhang, Julia Y.F. Chang, Yanqing Huang, Xiang Lin, Yongde Luo, Robert J. Schwartz, James F. Martin, Fen Wang. Circ Res. 2010;107(10):1209-19.

FGF10 controls the patterning of the tracheal cartilage rings via Shh by Frédéric G. Sala, Pierre-Marie Del Moral, Caterina Tiozzo, Denise Al Alam, David Warburton, Tracy Grikscheit, Jacqueline M. Veltmaat and Saverio Bellusci. Development (2010) 138, 273-282. doi: 10.1242/dev.05168.

The care and maintenance of your adviser by Hugh Kearns & Maria Gardiner Nature 2011; 469 (570) doi:10.1038/nj7331-570a (Open Access, yay again!)

The Wnt/beta-catenin pathway regulates cardiac valve formation by Hurlstone AF, Haramis AP, Wienholds E, Begthel H, Korving J, Van Eeden F, Cuppen E, Zivkovic D, Plasterk RH, Clevers H. Nature. 2003;425 (633-7).

Biallelic somatic and germline mutations in cerebral cavernous malformations (CCMs): evidence for a two-hit mechanism of CCM pathogenesis by Akers AL, Johnson E, Steinberg GK, Zabramski JM, Marchuk DA. Hum Mol Genet. 2009 Mar 1;18(5):919-30. PMID: 19088123 (Open Access, yay again!)

A two-hit mechanism causes cerebral cavernous malformations: complete inactivation of CCM1, CCM2 or CCM3 in affected endothelial cells by Pagenstecher A, Stahl S, Sure U, and Felbor U. Hum Mol Genet. 2009 Mar 1;18(5):911-8. PMID: 19088124 (Open Access, same issue)

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development by Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, Pleasance ED, Lau KW, Beare D, Stebbings LA, McLaren S, Lin ML, McBride DJ, Varela I, Nik-Zainal S, Leroy C, Jia M, Menzies A, Butler AP, Teague JW, Quail MA, Burton J, Swerdlow H, Carter NP, Morsberger LA, Iacobuzio-Donahue C, Follows GA, Green AR, Flanagan AM, Stratton MR, Futreal PA, Campbell PJ. Cell. 2011;144(1):27-40. PMID: 21215367.

Stringent requirement of a proper level of canonical WNT signalling activity for head formation in mouse embryo by Nicolas Fossat, Vanessa Jones, Poh-Lynn Khoo, Debora Bogani, Andrea Hardy, Kirsten Steiner, Mahua Mukhopadhyay, Heiner Westphal, Patrick M. Nolan, Ruth Arkell and Patrick P. L. Tam. Development (2011) 138, 667-676 doi:10.1242/dev.052803.

Ripply3, a Tbx1 repressor, is required for development of the pharyngeal apparatus and its derivatives in mice by Tadashi Okubo, Akinori Kawamura, Jun Takahashi, Hisato Yagi, Masae Morishima, Rumiko Matsuoka and Shinji Takada. Development (2011) 138, 339-348. doi: 10.1242/dev.054056.

Vax2 regulates retinoic acid distribution and cone opsin expression in the vertebrate eye by Giovanna Alfano, Ivan Conte, Tiziana Caramico, Raffaella Avellino, Benedetta Arnò, Maria Teresa Pizzo, Naoyuki Tanimoto, Susanne C. Beck, Gesine Huber, Pascal Dollé, Mathias W. Seeliger and Sandro Banfi.  Development 138, 261-271. doi: 10.1242/dev.051037.

Dishevelled-associated activator of morphogenesis 1 (Daam1) is required for heart morphogenesis by Deqiang Li, Mark A. Hallett, Wuqiang Zhu, Michael Rubart, Ying Liu, Zhenyun Yang, Hanying Chen, Laura S. Haneline, Rebecca J. Chan, Robert J. Schwartz, Loren J. Field, Simon J. Atkinson and Weinian Shou. Development (2011) 138, 303-315. doi: 10.1242/dev.055566.

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man by Timothy Ravasi, Harukazu Suzuki, Carlo Vittorio Cannistraci, Shintaro Katayama, Vladimir B. Bajic, Kai Tan, Altuna Akalin, Sebastian Schmeier, Mutsumi Kanamori-Katayama, Nicolas Bertin, Piero Carninci, Carsten O. Daub, Alistair R.R. Forrest, Julian Gough, Sean Grimmond, Jung-Hoon Han, Takehiro Hashimoto, Winston Hide, Oliver Hofmann, Atanas Kamburov, et al. Cell 2010, Volume 141(2)369. (Link is to the Resource – the atlas itself.)

…We have screened for physical interactions among the majority of human and mouse DNA-binding transcription factors (TFs). The complete networks contain 762 human and 877 mouse interactions. Analysis of the networks reveals that highly connected TFs are broadly expressed across tissues, and that roughly half of the measured interactions are conserved between mouse and human. The data highlight the importance of TF combinations for determining cell fate…

And because if there aren’t any photos, it didn’t happen, here is the obligatory furry-animal shot to sweeten the medicine. There was a deputy mayor of Bayonne (France, not New Jersey) on my right, and Pascal Ondarts on my left, a famous retired rugbyman, who baptized the tiger in my arms “Junot” at the behest of the circus Amar. They sponsor a patient group that itself supports my research in part. There have been other militant patient groups who have funded my work in the past and present, and I am grateful to all of them, and try to give them cause to be grateful to me in return.

Author and celebrity not a patch on a cute furry animal

Junot, the tiger cub, shows some alternate pigmentation for Naevus 2000 France-Europe

* And yet I am not supposed to, nor do I, spend all day on the computer. I am no longer even a blogger. I am back to being a developmental biologist and an amateur musician and a few other roles, and that is starting to feel good and natural again, even though I get twinges when I see the fuss around science blogging conferences. If only we could live many lives in parallel. It’s all I can do to keep a couple going.

About Heather

That French-American biomed researcher again.
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23 Responses to Open tabs

  1. Eva says:

    The tiger kitten is ADORABLE! It’s so cute when animals haven’t yet grown into their paws/head. Did it feel as soft as it looks? Was it heavy?

  2. Heather says:

    See the stars in my eyes? Yep, it’s as soft as it looks, and about as heavy as a fat cat the same size. And I didn’t even sneeze (I was terribly sensitized from the horses earlier).

  3. Frank says:

    Nice one Heather! I like the “open tabs” idea. Oh, and welcome to the OT guest blogger list.

    • Heather says:

      Thanks, Frank, for the comment and the welcome! Nothing to like about my multi-tab lifestyle, really, it’s my constant way of being on the Internet. My desk is much the same. Definitely horizontally organized.

  4. ricardipus says:

    Hey look – there’s a tiger cub!

    Oh, and Heather too… 😉

    Welcome to the OTR from over here too. And that is a truly impressive set of browser tabs – did you actually read all those papers? If so, I am in awe.

  5. Frank says:

    Richard – I think the point is that by leaving the tab open you don’t actually have to read it. That’s how it works for me anyway.

  6. Cath@VWXYNot? says:

    Do you have ANY IDEA how jealous I am that you got to hold a tiger cub? IMHO the only thing cuter than a tiger cub is a tiger cub with a baby orangutan sidekick. I would pay SO MUCH MONEY to take your place in that photo!

    I, too, open tabs to save articles for later. It does become a problem after a while… I try to clear them on lunch breaks, but I typically still have 3 or 4 open at the end of the week.

    • Heather says:

      You did give me a wee idea at the moment 🙂 But that photo is very effectively cute. Amazing how our minds want to anthropomorphize so badly. I can’t help it, even when I’m aware of it. Maybe it’s a common trait among animal lovers. We’ll ask Kristi sometime.

  7. cromercrox says:

    I’m sure there’ll always be a place here for you to get things off your chest if you feel you need to.

  8. Heather says:

    Thanks for the warm welcome into the fold, everyone. Time for the next Irregular to step up to the bat.

    @R – what Frank said. I’ve perused some of them enough to be able to close the tab after downloading the PDF, but right now four of the articles are still open, along with a bunch of other new stuff.

    Including the upload page for a grant mechanism, that as Steffi knows had no input from two of my three other partners until – get this – yesterday afternoon. Part of my writing this post was because I had given up on them. Submission: Monday, January 30th.

    We could have a group tab dump on Fridays, what say? Sometimes it’s fun to see what people have open on their desks. Purely voluntary.

  9. KristiV says:

    I’ll add my welcome too, Heather (though I still feel too new at OT to be doing so). Interesting news about the BRAF inhibitor; I hope it lives up to the initial promise. Lots of excellent papers, too – can’t look at them all, but I’ll definitely add the work on tracheal rings to my lecture on lung development in March.

    I used to keep up with the heart development research from Epstein’s lab, because they worked on the Nf1-deficient mouse models, but have lost track of that and many other things besides, unfortunately. My tabs are more likely to have DNA damage/repair papers these days – only have the chance to look at development papers when I’m updating lectures for my evo-devo course. *sigh* 😉

  10. chall says:

    oh, this was so much fun 🙂

    I ended up getting more tabs open since I am too curious not to click on some of (ok, almost all) the tabs you mention….. I too open tabs and then either down load the pdf “for further reading” or bookmark in my “maybe interesting later”folder that I keep. I clean that one out about once a month, since usually they are time-limited-interesting.

    And that photo is so cute!!

  11. Grant says:

    I usually do a tab dump, err structured procrastination, every Friday or so but I’ve now procrastinated enough that my structured procrastination is procrastinated. Terrifying.*

    (Actually it means I’m motivated on my grant application and my blog is in tatters.)

    Nice list, but I am standing strong and refuse to check out that article on combinatorial TFs, something related to part of my Ph.D. thesis work (some stuff I did on dimeric interfaces for some TFs). I’d want to know if they tested monomeric TFs, or the functional unit (in a lot of cases, dimers).

    Okkkk. Back to the reading…

    Good to see you blogging here.

    * Two different browsers open, with perhaps a 150 tabs open between them. Don’t ask 🙂

  12. Frank says:

    I just read a review of Instapaper and am wondering if this might help me to reduce my tendency to have too many tabs open of things I mean to read? It seems particularly useful in combination with an iPhone or iPad. Perhaps the real problem is lack of time to read things that are interesting but not essential?

    • Heather says:

      I agree about the main problem – and usually, the world continues spinning when we’ve missed reading certain things. It sounds really good when you have a commute using public transportation, and an intermittent connection. And, as you say, an iPhone. Maybe this is one to flag up to Henry.

  13. Steve Caplan says:

    Welcome from another newbie! I enjoyed the “The care and maintenance of your adviser” article: I wish my students would take care of me…

    • Heather says:

      Thanks, Steve,
      Yes, I was wondering who would pick up on it, and whether or not I should write a blurb about it, too (but I didn’t have the time). Don’t we all want to be taken care of!

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